kinome: Example Data from InfectX

Description Usage Format Value Note References Examples

Description

Data from gene knock-down experiments performed with 11 siRNA for 8 different pathogens. The data was generated by the InfectX consortium.

Usage

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Format

The data frame contains the microscope image readouts of 826 kinases knock-down experiments. For each gene cells were targeted by a total of 12 independent siRNAs coming from three manufactures: Ambion (3 siRNAs), Qiagen (4 siRNAs) and Dharmacon (4 siRNAs + 1 pool siRNA). All experiments were conducted for 8 different pathogens. Each row of the data frame corresponds to the result of one experiment.

GeneID ID of the gene that is knocked down.
GeneName Name of the gene that is knocked down.
company Company that provided the siRNA for knock-down.
siRNA Label to identify the different siRNA replicates that are used.
CellCount normalized image readout describing the number of cells in the well
InfectionIndex normalized image readout describing the number of infected cells in the well
weight_library weight denoting the quality of libraries. We assigned a higher weight to
Dharmacon Pooled and Ambion libraries (weight 2) than to the unpooled
libraries Dharmacon and Qiagen (weight 1).

Value

data.frame

Note

All of our screening data, including raw images, are available at the openBIS portal (http://infectx.ch/dataaccess).

References

Rämö, P., Drewek, A., Arrieumerlou, C., Beerenwinkel, N., Ben-Tekaya H., Cardel, B., Casanova, A., Conde-Alvarez. R., Cossart, P., Csucs, G., Eicher, S., Emmenlauer, M. Greber, U., Hardt, W.-D., Helenius, A., Kasper, C., Kaufmann, A., Kreibich, S., Kuebacher, A., Kunszt, P., Low, S.H., Mercer, J., Mudrak, D., Muntwiler, S., Pelkmans, L., Pizarro-Cerda, J., Podvinec, M., Pujadas, E., Rinn, B., Rouilly, V., Schmich F., Siebourg, J., Snijder, B., Stebler, M., Studer, G., Szczurek, E., Truttmann, M., von Mering, C., Vonderheit, A., Yakimovich, A., Buehlmann, P. and Dehio, C., Simultaneous analysis of large-scale RNAi screens for pathogen entry, BMC Genomics 15(1162): p.1471-2164. (2014)

Examples

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pmm documentation built on Nov. 8, 2020, 6:55 p.m.